rs1573815

Positions:

• chr3-52836116-G-A
• chr3-52836116-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001198974.3(STIMATE-MUSTN1):​c.880-2367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,458 control chromosomes in the GnomAD database, including 4,876 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (4864 hom., cov: 32)
  • Exomes 𝑓: 0.19 (12 hom.)
• Consequence: STIMATE-MUSTN1 NM_001198974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

Genes affected

STIMATE-MUSTN1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STIMATE-MUSTN1	NM_001198974.3	c.880-2367C>T		intron_variant			NP_001185903.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37382 AN: 151912 Hom.: 4864 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.244

GnomAD4 exome AF: 0.193 AC: 83 AN: 430 Hom.: 12 Cov.: 0 AF XY: 0.176 AC XY: 42 AN XY: 238

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.188

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.246 AC: 37409 AN: 152028 Hom.: 4864 Cov.: 32 AF XY: 0.248 AC XY: 18439 AN XY: 74294

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.246

Alfa AF: 0.269 Hom.: 1023

Bravo AF: 0.257

Asia WGS AF: 0.238 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1573815; hg19: chr3-52870132;